bioseq_handle.hpp

ncbi源码

    // inst.length
    void SetInst_Length(TInst_Length v) const;
    // inst.fuzz
    void SetInst_Fuzz(TInst_Fuzz& v) const;
    // inst.topology
    void SetInst_Topology(TInst_Topology v) const;
    // inst.strand
    void SetInst_Strand(TInst_Strand v) const;
    // inst.seq-data
    void SetInst_Seq_data(TInst_Seq_data& v) const;
    // inst.ext
    void SetInst_Ext(TInst_Ext& v) const;
    // inst.hist
    void SetInst_Hist(TInst_Hist& v) const;
    // annot
    //////////////////////////////////////////////////////////////////


    // Add/remove/replace annotations:
    CSeq_annot_EditHandle AttachAnnot(const CSeq_annot& annot) const;
    CSeq_annot_EditHandle CopyAnnot(const CSeq_annot_Handle& annot) const;
    CSeq_annot_EditHandle TakeAnnot(const CSeq_annot_EditHandle& annot) const;

    // Tree modification, target handle must be in the same TSE
    // entry.Which() must be e_not_set or e_Set.
    CBioseq_EditHandle MoveTo(const CSeq_entry_EditHandle& entry,
                              int index = -1) const;
    CBioseq_EditHandle MoveTo(const CBioseq_set_EditHandle& seqset,
                              int index = -1) const;

    CBioseq_EditHandle MoveToSeq(const CSeq_entry_EditHandle& entry) const;

    void Remove(void) const;

protected:
    friend class CScope_Impl;

    CBioseq_EditHandle(const CBioseq_Handle& h);

public: // non-public section
    CBioseq_Info& x_GetInfo(void) const;
};


/////////////////////////////////////////////////////////////////////////////
// CBioseq_Handle inline methods
/////////////////////////////////////////////////////////////////////////////


inline
CBioseq_Handle::CBioseq_Handle(void)
{
}


inline
const CSeq_id_Handle& CBioseq_Handle::GetSeq_id_Handle(void) const
{
    return m_Seq_id;
}


inline
CBioseq_Handle::operator bool(void)  const
{
    return m_Bioseq_Info;
}


inline
bool CBioseq_Handle::operator!(void) const
{
    return !m_Bioseq_Info;
}


inline
const CBioseq_ScopeInfo& CBioseq_Handle::x_GetScopeInfo(void) const
{
    return reinterpret_cast<const CBioseq_ScopeInfo&>(*m_Bioseq_Info);
}


inline
CBioseq_Info& CBioseq_EditHandle::x_GetInfo(void) const
{
    return const_cast<CBioseq_Info&>(CBioseq_Handle::x_GetInfo());
}


inline
CScope& CBioseq_Handle::GetScope(void) const 
{
    return m_Scope;
}


inline
bool CBioseq_Handle::operator!= (const CBioseq_Handle& h) const
{
    return !(*this == h);
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ---------------------------------------------------------------------------
* $Log: bioseq_handle.hpp,v $
* Revision 1000.4  2004/06/01 19:21:17  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.56
*
* Revision 1.56  2004/05/06 17:32:37  grichenk
* Added CanGetXXXX() methods
*
* Revision 1.55  2004/03/31 19:23:13  vasilche
* Fixed scope in CBioseq_Handle::GetEditHandle().
*
* Revision 1.54  2004/03/31 17:08:06  vasilche
* Implemented ConvertSeqToSet and ConvertSetToSeq.
*
* Revision 1.53  2004/03/29 20:13:05  vasilche
* Implemented whole set of methods to modify Seq-entry object tree.
* Added CBioseq_Handle::GetExactComplexityLevel().
*
* Revision 1.52  2004/03/25 19:27:43  vasilche
* Implemented MoveTo and CopyTo methods of handles.
*
* Revision 1.51  2004/03/24 18:30:28  vasilche
* Fixed edit API.
* Every *_Info object has its own shallow copy of original object.
*
* Revision 1.50  2004/03/16 21:01:32  vasilche
* Added methods to move Bioseq withing Seq-entry
*
* Revision 1.49  2004/03/16 15:47:26  vasilche
* Added CBioseq_set_Handle and set of EditHandles
*
* Revision 1.48  2004/02/06 16:07:26  grichenk
* Added CBioseq_Handle::GetSeq_entry_Handle()
* Fixed MapLocation()
*
* Revision 1.47  2003/11/28 15:13:24  grichenk
* Added CSeq_entry_Handle
*
* Revision 1.46  2003/11/17 16:03:12  grichenk
* Throw exception in CBioseq_Handle if the parent scope has been reset
*
* Revision 1.45  2003/11/10 18:12:43  grichenk
* Added MapLocation()
*
* Revision 1.44  2003/09/30 16:21:59  vasilche
* Updated internal object manager classes to be able to load ID2 data.
* SNP blobs are loaded as ID2 split blobs - readers convert them automatically.
* Scope caches results of requests for data to data loaders.
* Optimized CSeq_id_Handle for gis.
* Optimized bioseq lookup in scope.
* Reduced object allocations in annotation iterators.
* CScope is allowed to be destroyed before other objects using this scope are
* deleted (feature iterators, bioseq handles etc).
* Optimized lookup for matching Seq-ids in CSeq_id_Mapper.
* Added 'adaptive' option to objmgr_demo application.
*
* Revision 1.43  2003/09/05 17:29:39  grichenk
* Structurized Object Manager exceptions
*
* Revision 1.42  2003/08/27 14:28:50  vasilche
* Reduce amount of object allocations in feature iteration.
*
* Revision 1.41  2003/07/15 16:14:06  grichenk
* CBioseqHandle::IsSynonym() made public
*
* Revision 1.40  2003/06/19 18:23:44  vasilche
* Added several CXxx_ScopeInfo classes for CScope related information.
* CBioseq_Handle now uses reference to CBioseq_ScopeInfo.
* Some fine tuning of locking in CScope.
*
* Revision 1.38  2003/05/20 15:44:36  vasilche
* Fixed interaction of CDataSource and CDataLoader in multithreaded app.
* Fixed some warnings on WorkShop.
* Added workaround for memory leak on WorkShop.
*
* Revision 1.37  2003/04/24 16:12:37  vasilche
* Object manager internal structures are splitted more straightforward.
* Removed excessive header dependencies.
*
* Revision 1.36  2003/03/27 19:39:34  grichenk
* +CBioseq_Handle::GetComplexityLevel()
*
* Revision 1.35  2003/03/21 19:22:48  grichenk
* Redesigned TSE locking, replaced CTSE_Lock with CRef<CTSE_Info>.
*
* Revision 1.34  2003/03/18 21:48:27  grichenk
* Removed obsolete class CAnnot_CI
*
* Revision 1.33  2003/03/18 14:46:35  grichenk
* Set limit object type to "none" if the object is null.
*
* Revision 1.32  2003/03/14 19:10:33  grichenk
* + SAnnotSelector::EIdResolving; fixed operator=() for several classes
*
* Revision 1.31  2003/03/12 20:09:30  grichenk
* Redistributed members between CBioseq_Handle, CBioseq_Info and CTSE_Info
*
* Revision 1.30  2003/02/27 14:35:32  vasilche
* Splitted PopulateTSESet() by logically independent parts.
*
* Revision 1.29  2003/01/23 19:33:57  vasilche
* Commented out obsolete methods.
* Use strand argument of CSeqVector instead of creation reversed seqmap.
* Fixed ordering operators of CBioseqHandle to be consistent.
*
* Revision 1.28  2003/01/22 20:11:53  vasilche
* Merged functionality of CSeqMapResolved_CI to CSeqMap_CI.
* CSeqMap_CI now supports resolution and iteration over sequence range.
* Added several caches to CScope.
* Optimized CSeqVector().
* Added serveral variants of CBioseqHandle::GetSeqVector().
* Tried to optimize annotations iterator (not much success).
* Rewritten CHandleRange and CHandleRangeMap classes to avoid sorting of list.
*
* Revision 1.27  2002/12/26 20:51:35  dicuccio
* Added Win32 export specifier
*
* Revision 1.26  2002/12/26 16:39:21  vasilche
* Object manager class CSeqMap rewritten.
*
* Revision 1.25  2002/11/08 22:15:50  grichenk
* Added methods for removing/replacing annotations
*
* Revision 1.24  2002/09/03 21:26:58  grichenk
* Replaced bool arguments in CSeqVector constructor and getters
* with enums.
*
* Revision 1.23  2002/08/23 16:49:06  grichenk
* Added warning about using CreateResolvedSeqMap()
*
* Revision 1.22  2002/07/08 20:50:56  grichenk
* Moved log to the end of file
* Replaced static mutex (in CScope, CDataSource) with the mutex
* pool. Redesigned CDataSource data locking.
*
* Revision 1.21  2002/06/12 14:39:00  grichenk
* Renamed enumerators
*
* Revision 1.20  2002/06/06 19:36:02  clausen
* Added GetTitle()
*
* Revision 1.19  2002/05/31 17:52:58  grichenk
* Optimized for better performance (CTSE_Info uses atomic counter,
* delayed annotations indexing, no location convertions in
* CAnnot_Types_CI if no references resolution is required etc.)
*
* Revision 1.18  2002/05/21 18:39:27  grichenk
* CBioseq_Handle::GetResolvedSeqMap() -> CreateResolvedSeqMap()
*
* Revision 1.17  2002/05/06 03:30:35  vakatov
* OM/OM1 renaming
*
* Revision 1.16  2002/05/03 18:35:36  grichenk
* throw -> THROW1_TRACE
*
* Revision 1.15  2002/04/23 19:01:06  grichenk
* Added optional flag to GetSeqVector() and GetSequenceView()
* for switching to IUPAC encoding.
*
* Revision 1.14  2002/04/22 20:06:58  grichenk
* +GetSequenceView(), +x_IsSynonym()
*
* Revision 1.13  2002/04/18 20:35:10  gouriano
* correction in comment
*
* Revision 1.12  2002/04/11 12:07:28  grichenk
* Redesigned CAnnotTypes_CI to resolve segmented sequences correctly.
*
* Revision 1.11  2002/03/19 19:17:33  gouriano
* added const qualifier to GetTitle and GetSeqVector
*
* Revision 1.10  2002/03/15 18:10:04  grichenk
* Removed CRef<CSeq_id> from CSeq_id_Handle, added
* key to seq-id map th CSeq_id_Mapper
*
* Revision 1.9  2002/03/04 15:08:43  grichenk
* Improved CTSE_Info locks
*
* Revision 1.8  2002/02/21 19:27:00  grichenk
* Rearranged includes. Added scope history. Added searching for the
* best seq-id match in data sources and scopes. Updated tests.
*
* Revision 1.7  2002/02/07 21:27:33  grichenk
* Redesigned CDataSource indexing: seq-id handle -> TSE -> seq/annot
*
* Revision 1.6  2002/02/01 21:49:10  gouriano
* minor changes to make it compilable and run on Solaris Workshop
*
* Revision 1.5  2002/01/29 17:05:53  grichenk
* GetHandle() -> GetKey()
*
* Revision 1.4  2002/01/28 19:45:33  gouriano
* changed the interface of BioseqHandle: two functions moved from Scope
*
* Revision 1.3  2002/01/23 21:59:29  grichenk
* Redesigned seq-id handles and mapper
*
* Revision 1.2  2002/01/16 16:26:36  gouriano
* restructured objmgr
*
* Revision 1.1  2002/01/11 19:04:00  gouriano
* restructured objmgr
*
*
* ===========================================================================
*/

#endif  // BIOSEQ_HANDLE__HPP